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Zhang S, Wang J, Liu Y, Xu Z. Multiple strategies to improve extracellular secretion and activity of feruloyl esterase. Int J Biol Macromol 2024; 269:132082. [PMID: 38705319 DOI: 10.1016/j.ijbiomac.2024.132082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 04/14/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Feruloyl esterase has a wide range of applications, but there are still problems with low enzyme yield and activity, and complex purification steps. Our previous research found Lactobacillus amylovorus feruloyl esterase could be secreted extracellular in Escherichia coli. In this study, multiple strategies were implemented to maximize the extracellular production of feruloyl esterase with improved activity in E. coli. Firstly, codon-optimized feruloyl esterase was obtained based on the preference of E. coli, resulting in 41.97 % increase in extracellular secretion. Furthermore, by cascading T7 promoters, replacing the 5' UTR, randomly mutating the N-terminal sequence, and co-expressing secretory cofactors, the extracellular secretion was increased by 36.46 %, 31.25 %, 20.66 % and 25.75 %, respectively. Moreover, the feruloyl esterase were mutated to improve the substrate affinity and activity. The catalytic efficiency of Fae-Q134T and Fae-Q198A increased by 4.62-fold and 5.42-fold. Combining above strategies, extracellular feruloyl esterase activity was increased from 2013.70 U/L to 10,349.04 U/L. These results indicated that the activity and yield of feruloyl esterase secreted by E. coli were significantly increased, which laid a foundation for its industrial application.
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Affiliation(s)
- Susu Zhang
- College of Life Science, Shandong Normal University, Jinan 250358, PR China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, PR China
| | - Jiapeng Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China; Department of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China
| | - Yaohan Liu
- College of Life Science, Shandong Normal University, Jinan 250358, PR China
| | - Zhenshang Xu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China; Department of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China.
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2
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Hafiz Rothi M, Sarkar GC, Haddad JA, Mitchell W, Ying K, Pohl N, Sotomayor-Mena RG, Natale J, Dellacono S, Gladyshev VN, Lieberman Greer E. The 18S rRNA Methyltransferase DIMT-1 Regulates Lifespan in the Germline Later in Life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594211. [PMID: 38798397 PMCID: PMC11118296 DOI: 10.1101/2024.05.14.594211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Ribosome heterogeneity has emerged as an important regulatory control feature for determining which proteins are synthesized, however, the influence of age on ribosome heterogeneity is not fully understood. Whether mRNA transcripts are selectively translated in young versus old cells and whether dysregulation of this process drives organismal aging is unknown. Here we examined the role of ribosomal RNA (rRNA) methylation in maintaining appropriate translation as organisms age. In a directed RNAi screen, we identified the 18S rRNA N6'-dimethyl adenosine (m6,2A) methyltransferase, dimt-1, as a regulator of C. elegans lifespan and stress resistance. Lifespan extension induced by dimt-1 deficiency required a functional germline and was dependent on the known regulator of protein translation, the Rag GTPase, raga-1, which links amino acid sensing to the mechanistic target of rapamycin complex (mTORC)1. Using an auxin-inducible degron tagged version of dimt-1, we demonstrate that DIMT-1 functions in the germline after mid-life to regulate lifespan. We further found that knock-down of dimt-1 leads to selective translation of transcripts important for stress resistance and lifespan regulation in the C. elegans germline in mid-life including the cytochrome P450 daf-9, which synthesizes a steroid that signals from the germline to the soma to regulate lifespan. We found that dimt-1 induced lifespan extension was dependent on the daf-9 signaling pathway. This finding reveals a new layer of proteome dysfunction, beyond protein synthesis and degradation, as an important regulator of aging. Our findings highlight a new role for ribosome heterogeneity, and specific rRNA modifications, in maintaining appropriate translation later in life to promote healthy aging.
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Affiliation(s)
- M. Hafiz Rothi
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Gautam Chandra Sarkar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Joseph Al Haddad
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston MA 02115, USA
| | - Kejun Ying
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Nancy Pohl
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Roberto G. Sotomayor-Mena
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Julia Natale
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Scarlett Dellacono
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston MA 02115, USA
| | - Eric Lieberman Greer
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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Bicknell AA, Reid DW, Licata MC, Jones AK, Cheng YM, Li M, Hsiao CJ, Pepin CS, Metkar M, Levdansky Y, Fritz BR, Andrianova EA, Jain R, Valkov E, Köhrer C, Moore MJ. Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay. Cell Rep 2024; 43:114098. [PMID: 38625793 DOI: 10.1016/j.celrep.2024.114098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/24/2024] [Accepted: 03/27/2024] [Indexed: 04/18/2024] Open
Abstract
Developing an effective mRNA therapeutic often requires maximizing protein output per delivered mRNA molecule. We previously found that coding sequence (CDS) design can substantially affect protein output, with mRNA variants containing more optimal codons and higher secondary structure yielding the highest protein outputs due to their slow rates of mRNA decay. Here, we demonstrate that CDS-dependent differences in translation initiation and elongation rates lead to differences in translation- and deadenylation-dependent mRNA decay rates, thus explaining the effect of CDS on mRNA half-life. Surprisingly, the most stable and highest-expressing mRNAs in our test set have modest initiation/elongation rates and ribosome loads, leading to minimal translation-dependent mRNA decay. These findings are of potential interest for optimization of protein output from therapeutic mRNAs, which may be achieved by attenuating rather than maximizing ribosome load.
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Affiliation(s)
| | - David W Reid
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | | | | | - Yi Min Cheng
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | - Mengying Li
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | | | | | - Mihir Metkar
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | - Yevgen Levdansky
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Brian R Fritz
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | | | - Ruchi Jain
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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Yang S, Zhang T, Ge Y, Yin L, Pu Y, Liang G. Inhalation exposure to polystyrene nanoplastics induces chronic obstructive pulmonary disease-like lung injury in mice through multi-dimensional assessment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123633. [PMID: 38423272 DOI: 10.1016/j.envpol.2024.123633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/10/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Nanoplastics are widely distributed in indoor and outdoor air and can be easily inhaled into human lungs. However, limited studies have investigated the impact of nanoplastics on inhalation toxicities, especially on the initiation and progression of chronic obstructive pulmonary disease (COPD). To fill the gap, the present study used oronasal aspiration to develop mice models. Mice were exposed to polystyrene nanoplastics (PS-NPs) at three concentrations, as well as the corresponding controls, for acute, subacute, and subchronic exposure. As a result, PS-NPs could accumulate in exposed mice lungs and influence lung organ coefficient. Besides, PS-NPs induced local and systemic oxidative stress, inflammation, and protease-antiprotease imbalance, resulting in decreased respiratory function and COPD-like lesions. Meanwhile, PS-NPs could trigger the subcellular mechanism to promote COPD development by causing mitochondrial dysfunctions and endoplasmic reticulum (ER) stress. Mechanistically, ferroptosis played an important role in the COPD-like lung injury induced by PS-NPs. In summary, the present study comprehensively and systematically indicates that PS-NPs can damage human respiratory health and increase the risk for COPD.
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Affiliation(s)
- Sheng Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China; Institute of Biomedical Devices (Suzhou), Southeast University, Suzhou, 215163, China.
| | - Tianyi Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China; Institute of Biomedical Devices (Suzhou), Southeast University, Suzhou, 215163, China.
| | - Yiling Ge
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China; Institute of Biomedical Devices (Suzhou), Southeast University, Suzhou, 215163, China.
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China.
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China.
| | - Geyu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China.
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Kazmi I, Altamimi ASA, Afzal M, Majami AA, Abbasi FA, Almalki WH, Alzera SI, Kukreti N, Fuloria NK, Fuloria S, Sekar M, Abida. Non-coding RNAs: Emerging biomarkers and therapeutic targets in ulcerative colitis. Pathol Res Pract 2024; 253:155037. [PMID: 38160482 DOI: 10.1016/j.prp.2023.155037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Ulcerative colitis (UC) is a persistent inflammatory condition affecting the colon's mucosal lining, leading to chronic bowel inflammation. Despite extensive research, the precise molecular mechanisms underlying UC pathogenesis remain elusive. NcRNAs form a category of functional RNA molecules devoid of protein-coding capacity. They have recently surfaced as pivotal modulators of gene expression and integral participants in various pathological processes, particularly those related to inflammatory disorders. The diverse classes of ncRNAs, encompassing miRNAs, circRNAs, and lncRNAs, have been implicated in UC. It highlights their involvement in key UC-related processes, such as immune cell activation, epithelial barrier integrity, and the production of pro-inflammatory mediators. ncRNAs have been identified as potential biomarkers for UC diagnosis and monitoring disease progression, offering promising avenues for personalized medicine. This approach may pave the way for novel, more specific treatments with reduced side effects, addressing the current limitations of conventional therapies. A comprehensive understanding of the interplay between ncRNAs and UC will advance our knowledge of the disease, potentially leading to more effective and personalized treatments for patients suffering from this debilitating condition. This review explores the pivotal role of ncRNAs in the context of UC, shedding light on their possible targets for diagnosis, prognosis, and therapeutic interventions.
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Affiliation(s)
- Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | | | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Abdullah A Majami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fahad Al Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzera
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Al-Jouf, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | | | - Shivkanya Fuloria
- Faculty of Pharmacy, AIMST University, Bedong 08100, Kedah, Malaysia
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| | - Abida
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
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Lafortune P, Zahid K, Ploszaj M, Awadalla E, Carroll TP, Geraghty P. Testing Alpha-1 Antitrypsin Deficiency in Black Populations. Adv Respir Med 2023; 92:1-12. [PMID: 38392031 PMCID: PMC10886060 DOI: 10.3390/arm92010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 02/24/2024]
Abstract
Alpha-1 antitrypsin (AAT) deficiency (AATD) is an under-recognized hereditary disorder and a significant cause of chronic obstructive pulmonary disease (COPD), a disease that contributes to global mortality. AAT is encoded by the SERPINA1 gene, and severe mutation variants of this gene increase the risk of developing COPD. AATD is more frequently screened for in non-Hispanic White populations. However, AATD is also observed in other ethnic groups and very few studies have documented the mutation frequency in these other ethnic populations. Here, we review the current literature on AATD and allele frequency primarily in Black populations and discuss the possible clinical outcomes of low screening rates in a population that experiences poor health outcomes and whether the low frequency of AATD is related to a lack of screening in this population or a truly low frequency of mutations causing AATD. This review also outlines the harmful SERPINA1 variants, the current epidemiology knowledge of AATD, health inequity in Black populations, AATD prevalence in Black populations, the clinical implications of low screening of AATD in this population, and the possible dangers of not diagnosing or treating AATD.
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Affiliation(s)
- Pascale Lafortune
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
| | - Kanza Zahid
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
| | - Magdalena Ploszaj
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
| | - Emilio Awadalla
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
| | - Tomás P. Carroll
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
- Alpha-1 Foundation Ireland, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Patrick Geraghty
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
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7
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Maslakova AA, Golyshev SA, Potashnikova DM, Moisenovich AM, Orlovsky IV, Smirnova OV, Rubtsov MA. SERPINA1 long transcripts produce non-secretory alpha1-antitrypsin isoform: In vitro translation in living cells. Int J Biol Macromol 2023; 241:124433. [PMID: 37086761 DOI: 10.1016/j.ijbiomac.2023.124433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/24/2023]
Abstract
SERPINA1 is a well-studied serpin gene due to its dramatic impact on human health. Translation initiation at the main SERPINA1 start codon produces the only known alpha1-antitrypsin (AAT) isoform intended for secretion. AAT performs essential functions by inhibiting proteases and modulating immunity. However, SERPINA1 expression at the level of translation is not sufficiently studied. Here we hypothesize that the main SERPINA1 ORF can be alternatively translated, producing a non-secretory AAT isoform by either masking or excluding a signal peptide. We defined SERPINA1 long mRNA isoforms specific for prostate (DU145) and liver (HepG2) cell lines and studied their individual expression by in vitro assay. We found that all long transcripts produce both glycosylated secretory AAT-eGFP fusion protein and non-glycosylated intracellular AAT-eGFP (initiated from an alternative AUG-2 start codon), with the proportion regulated by the SERPINA1 5'-UTR. Both fusion proteins localize to distinct cellular compartments: in contrast to a fusion with the secretory AAT accumulating in the ER, the intracellular one exhibits nuclear-cytoplasmic shuttling. We detected putative endogenous AAT isoform enriching the nuclear speckles. CONCLUSION: Alternative translation initiation might be a mechanism through which SERPINA1 expands the biological diversity of its protein products. Our findings open up new prospects for the study of SERPINA1 gene expression.
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Affiliation(s)
- A A Maslakova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia.
| | - S A Golyshev
- A.N. Belozersky Institute of Physical and Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - D M Potashnikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - A M Moisenovich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - I V Orlovsky
- Research Institute of Molecular and Cellular Medicine, Рeoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya, Moscow 117198, Russia
| | - O V Smirnova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - M A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya, Moscow 119991, Russia
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